The folly of absolute dichotomies

Divide and conquer (nothing)

Divisiveness is becoming quickly apparent as a plague on the modern era. The segregation and categorisation of people – whether politically, spiritually or morally justified – permeates throughout the human condition and in how we process the enormity of the Homo sapien population. The idea that the antithetic extremes form two discrete categories (for example, the waning centrist between ‘left’ vs. ‘right’ political perspectives) is widely employed in many aspects of the world.

But how pervasive is this pattern? How well can we summarise, divide and categorise people? For some things, this would appear innately very easy to do – one of the most commonly evoked divisions in people is that between men and women. But the increasingly charged debate around concepts of both gender and sex (and sexuality as a derivative, somewhat interrelated concept) highlights the inconsistency of this divide.

The ‘sex’ and ‘gender’ arguments

The most commonly used argument against ‘alternative’ concepts of either gender of sex – the binary states of a ‘man’ with a ‘male’ body and a ‘female’ with a ‘female’ body – is often based on some perception of “biologically reality.” As a (trainee) biologist, let me make this apparently clear that such confidence and clarity of “reality” in many, if not all, biological subdisciplines is absurd (e.g. “nature vs. nurture”). Biologists commonly acknowledge (and rely upon) the realisation that life in all of its constructs is unfathomably diverse, unique, and often difficult to categorise. Any impression of being able to do so is a part of the human limitation to process concepts without boundaries.

Genderbread-Person figure
A great example of the complex nature of human sex and gender. You’ll notice that each category is itself a spectrum: even Biological Sex is not a clearly binary system. In fact, even this representation likely simplifies the complexity of human identity and sexuality given that each category is only a single linear scale (e.g. pansexuality and asexuality aren’t on the Sexual Orientation gradient), but nevertheless is a good summary. Source: It’s Pronounced METROsexual.

Gender as a binary

In terms of gender identity, I think this is becoming (slowly) more accepted over time. That most people have a gender identity somewhere along a multidimensional spectrum is not, for many people, a huge logical leap. Trans people are not mentally ill, not all ‘men’ identify as ‘men’ and certainly not all ‘men’ identify as a ‘man’ under the same characteristics or expression. Human psychology is beautifully complex and to reduce people down to the most simplistic categories is, in my humble opinion, a travesty. The single-variable gender binary cannot encapsulate the full depth of any single person’s identity or personality, and this biologically makes sense.

Sex as a binary

As an extension of the gender debate, sex itself has often been relied upon as the last vestige of some kind of sexual binary. Even for those more supported of trans people, sex is often described as some concrete, biologically, genetically-encoded trait which conveniently falls into its own binary system. Thus, instead of a single binary, people are reduced down to a two-character matrix of sex and gender.

Gender and sex table.jpg
A representative table of the “2 Character Sex and Gender” composition. Although slightly better at allowing for complexity in people’s identities, having 2 binaries instead of 1 doesn’t encapsulate the full breadth of diversity in either sex or gender.

However, the genetics of the definition and expression of sex is in itself a complex network of the expression of different genes and the presence of different chromosomes. Although high-school level biology teaches us that men are XY and women are XX genetically, individual genes within those chromosomes can alter the formation of different sexual organs and the development of a person. Furthermore, additional X or Y chromosomes can further alter the way sexual development occurs in people. Many people who fall in between the two ends of the gender spectrum of Male and Female identify as ‘intersex’.

DSD types table.jpg
A list of some of the known types of ‘Disorders of Sex Development’ (DSDs) which can lead to non-binary sex development in many different ways. Within these categories, there may be multiple genetic mechanisms (e.g. specific mutations) underlying the symptoms. It’s also important to note that while DSD medically describes the conditions of many people, it can be offensive/inappropriate to many intersex people (‘disorder’ can be a heavy word). Source: El-Sherbiny (2013).

You might be under the impression that these are rare ‘genetic disorders’, and don’t count as “real people” (decidedly not my words). But the reality is that intersex people are relatively common throughout the world, and occur roughly as frequently as true redheads or green eyes. Thus, the idea that excluding intersex people from the rest of societal definitions has very little merit, especially from a scientific point of view. Instead, allowing our definitions of both sex and gender to be broad and flexible allows us to incorporate the biological reality of the immense diversity of the world, even just within our own species.

Absolute species concepts

Speaking of species, and relating this paradigm of dichotomy to potentially less politically charged concepts, species themselves are a natural example on the inaccuracy of absolutism. This idea is not a new one, either within The G-CAT or within the broad literature, and species identity has long been regarded as a hive of grey areas. The sheer number of ways a group of organisms can be divided into species (or not, as the case may be) lends to the idea that simplified definitions of what something is or is not will rarely be as accurate as we hope. Even the most commonly employed of characteristics – such as those of the Biological Species Conceptcannot be applied to a number of biological systems such as asexually-reproducing species or complex cases of isolation.

Speciation continuum figure
A figure describing the ‘speciation continuum’ from a previous post on The G-CAT. Now imagine that each Species Concept has it’s own vague species boundary (dotted line): draw 30 of them over the top of one another, and try to pick the exact cut-off between the red and green areas. Even using the imagination, this would be difficult.

The diversity of Life

Anyone who argues a biological basis for these concepts is taking the good name of biological science hostage. Diversity underpins the most core aspects of biology (e.g. evolution, communities and ecosystems, medicine) and is a real attribute of living in a complicated world. Downscaling and simplifying the world to the ‘black’ and the ‘white’ discredits the wonder of biology, and acknowledging the ‘outliers’ (especially those that are not actually so far outside the boxes we have drawn) of any trends we may observe in nature is important to understand the complexity of life on Earth. Even if individual components of this post seem debatable to you: always remember that life is infinitely more complex and colourful than we can even imagine, and all of that is underpinned by diversity in one form or another.

An identity crisis: using genomics to determine species identities

This is the fourth (and final) part of the miniseries on the genetics and process of speciation. To start from Part One, click here.

In last week’s post, we looked at how we can use genetic tools to understand and study the process of speciation, and particularly the transition from populations to species along the speciation continuum. Following on from that, the question of “how many species do I have?” can be further examined using genetic data. Sometimes, it’s entirely necessary to look at this question using genetics (and genomics).

Cryptic species

A concept that I’ve mentioned briefly previously is that of ‘cryptic species’. These are species which are identifiable by their large genetic differences, but appear the same based on morphological, behavioural or ecological characteristics. Cryptic species often arise when a single species has become fragmented into several different populations which have been isolated for a long time from another. Although they may diverge genetically, this doesn’t necessarily always translate to changes in their morphology, ecology or behaviour, particularly if these are strongly selected for under similar environmental conditions. Thus, we need to use genetic methods to be able to detect and understand these species, as well as later classify and describe them.

Cryptic species fish
An example of cryptic species. All four fish in this figure are morphologically identical to one another, but they differ in their underlying genetic variation (indicated by the different colours of DNA). Thus, from looking at these fish alone we would not perceive any differences, but their genetic make-up might suggest that there are more than one species…
Cryptic species heatmap example
The level of genetic differentiation between the fish in the above example. The phylogenies on the left and top of the figure demonstrate the evolutionary relationships of these four fish. The matrix shows a heatmap of the level of differences between different pairwise comparisons of all four fish: red squares indicate zero genetic differences (such as when comparing a fish to itself; the middle diagonal) whilst yellow squares indicate increasingly higher levels of genetic differentiation (with bright yellow = all differences). By comparing the different fish together, we can see that Fish 1 and 2, and Fish 3 and 4, are relatively genetically similar to one another (red-deep orange). However, other comparisons show high level of genetic differences (e.g. 1 vs 3 and 1 vs 4). Based on this information, we might suggest that Fish 1 and 2 belong to one cryptic species (A) and Fish 3 and 4 belong to a second cryptic species (B).

Genetic tools to study species: the ‘Barcode of Life’

A classically employed method that uses DNA to detect and determine species is referred to as the ‘Barcode of Life’. This uses a very specific fragment of DNA from the mitochondria of the cell: the cytochrome c oxidase I gene, CO1. This gene is made of 648 base pairs and is found pretty well universally: this and the fact that CO1 evolves very slowly make it an ideal candidate for easily testing the identity of new species. Additionally, mitochondrial DNA tends to be a bit more resilient than its nuclear counterpart; thus, small or degraded tissue samples can still be sequenced for CO1, making it amenable to wildlife forensics cases. Generally, two sequences will be considered as belonging to different species if they are certain percentage different from one another.

Annotated mitogeome
The full (annotated) mitochondrial genome of humans, with the different genes within it labelled. The CO1 gene is labelled with the red arrow (sometimes also referred to as COX1) whilst blue arrows point to other genes often used in phylogenetic or taxonomic studies, depending on the group or species in question.

Despite the apparent benefits of CO1, there are of course a few drawbacks. Most of these revolve around the mitochondrial genome itself. Because mitochondria are passed on from mother to offspring (and not at all from the father), it reflects the genetic history of only one sex of the species. Secondly, the actual cut-off for species using CO1 barcoding is highly contentious and possibly not as universal as previously suggested. Levels of sequence divergence of CO1 between species that have been previously determined to be separate (through other means) have varied from anywhere between 2% to 12%. The actual translation of CO1 sequence divergence and species identity is not all that clear.

Gene tree – species tree incongruences

One particularly confounding aspect of defining species based on a single gene, and with using phylogenetic-based methods, is that the history of that gene might not actually be reflective of the history of the species. This can be a little confusing to think about but essentially leads to what we call “gene tree – species tree incongruence”. Different evolutionary events cause different effects on the underlying genetic diversity of a species (or group of species): while these may be predictable from the genetic sequence, different parts of the genome might not be as equally affected by the same exact process.

A classic example of this is hybridisation. If we have two initial species, which then hybridise with one another, we expect our resultant hybrids to be approximately made of 50% Species A DNA and 50% Species B DNA (if this is the first generation of hybrids formed; it gets a little more complicated further down the track). This means that, within the DNA sequence of the hybrid, 50% of it will reflect the history of Species A and the other 50% will reflect the history of Species B, which could differ dramatically. If we randomly sample a single gene in the hybrid, we will have no idea if that gene belongs to the genealogy of Species A or Species B, and thus we might make incorrect inferences about the history of the hybrid species.

Gene tree incongruence figure
A diagram of gene tree – species tree incongruence. Each individual coloured line represents a single gene as we trace it back through time; these are mostly bound within the limits of species divergences (the black borders). For many genes (such as the blue ones), the genes resemble the pattern of species divergences very well, albeit with some minor differences in how long ago the splits happened (at the top of the branches). However, the red genes contrast with this pattern, with clear movement across species (from and into B): this represents genes that have been transferred by hybridisation. The green line represents a gene affected by what we call incomplete lineage sorting; that is, we cannot trace it back far enough to determine exactly how/when it initially diverged and so there are still two separate green lines at the very top of the figure. You can think of each line as a separate phylogenetic tree, with the overarching species tree as the average pattern of all of the genes.

There are a number of other processes that could similarly alter our interpretations of evolutionary history based on analysing the genetic make-up of the species. The best way to handle this is simply to sample more genes: this way, the effect of variation of evolutionary history in individual genes is likely to be overpowered by the average over the entire gene pool. We interpret this as a set of individual gene trees contained within a species tree: although one gene might vary from another, the overall picture is clearer when considering all genes together.

Species delimitation

In earlier posts on The G-CAT, I’ve discussed the biogeographical patterns unveiled by my Honours research. Another key component of that paper involved using statistical modelling to determine whether cryptic species were present within the pygmy perches. I didn’t exactly elaborate on that in that section (mostly for simplicity), but this type of analysis is referred to as ‘species delimitation’. To try and simplify complicated analyses, species delimitation methods evaluate possible numbers and combinations of species within a particular dataset and provides a statistical value for which configuration of species is most supported. One program that employs species delimitation is Bayesian Phylogenetics and Phylogeography (BPP): to do this, it uses a plethora of information from the genetics of the individuals within the dataset. These include how long ago the different populations/species separated; which populations/species are most related to one another; and a pre-set minimum number of species (BPP will try to combine these in estimations, but not split them due to computational restraints). This all sounds very complex (and to a degree it is), but this allows the program to give you a statistical value for what is a species and what isn’t based on the genetics and statistical modelling.

Vittata cryptic species
The cryptic species of pygmy perches identified within my research paper. This represents part of the main phylogenetic tree result, with the estimates of divergence times from other analyses included. The pictures indicate the physiology of the different ‘species’: Nannoperca pygmaea is morphologically different to the other species of Nannoperca vittata. Species delimitation analysis suggested all four of these were genetically independent species; at the very least, it is clear that there must be at least 2 species of Nannoperca vittata since is more related to N. pygmaea than to other N. vittata species. Photo credits: N. vittata = Chris Lamin; N. pygmaea = David Morgan.

The end result of a BPP run is usually reported as a species tree (e.g. a phylogenetic tree describing species relationships) and statistical support for the delimitation of species (0-1 for each species). Because of the way the statistical component of BPP works, it has been found to give extremely high support for species identities. This has been criticised as BPP can, at time, provide high statistical support for genetically isolated lineages (i.e. divergent populations) which are not actually species.

Improving species identities with integrative taxonomy

Due to this particular drawback, and the often complex nature of species identity, using solely genetic information such as species delimitation to define species is extremely rare. Instead, we use a combination of different analytical techniques which can include genetic-based evaluations to more robustly assign and describe species. In my own paper example, we suggested that up to three ‘species’ of N. vittata that were determined as cryptic species by BPP could potentially exist pending on further analyses. We did not describe or name any of the species, as this would require a deeper delve into the exact nature and identity of these species.

As genetic data and analytical techniques improve into the future, it seems likely that our ability to detect and determine species boundaries will also improve. However, the additional supported provided by alternative aspects such as ecology, behaviour and morphology will undoubtedly be useful in the progress of taxonomy.